2 things stock markets and at least 2 vr or "happy" structures.

The majority of your income comes from taxes. Taxes come from your population. Try to have a high population and keep that population happy(100% morale for as long as you can afford from turn 1, super breeder works best with this). Then when you can't afford to keep your population exceptionally happy, raise taxes and take your morale down to 46%.

You'll find that you make more money by raising a larger happy population and then taxing them heavily then to tax the smaller population heavily early on. Why? Because then you're taxing less people and that heavy taxation early on will cause very slow pop growth and bring you much less money and later expansion of your empire will demand more funds which you won't have.

Also, research those higher types of governments. They come with bonuses to your economy. 10%-30%.

trade routes (this is only a minor +)

Build A LOT of economy improvments. I do something like 50% of each planet. Except for the Research and production capitals. On smaller PQ worlds i just have one farm and all the rest economy buildings. The tech time to get to stock exchanges isn't too long.

I don't think this is your problem, but dont build too large of a military until you have the money to keep it.

Okay..this is what i found out to solve the money problem. I was always in your situation before. So i figured that for each planet you are colonizing, have two entertainment center, forget building any farms. Have at least one research lab, and have one factory if you wish. But you don't need it for each of your planet.

Next, for the spending slider, make sure you drop the miltary slider to almost zero, and then increase your social production to a resonable level, then slowly increase your reserach slider. Do this gradually until both research and social production slider is at max. At the same time, increase your productivity slider gradually, while trying to keep your approval rating to be at 71 percent. As time goes on, your economy should always remain positive. WHile you are doing all this, make sure you the following techs researched as quickly as possible, Xeno Entertainment, and xeno economics. First gives you boost for morale, second boosts your economics. On more difficut settings, it is not enough that you have a positive economy going at all times, you have to expand to a resonable level in terms of number of planets you have.

ALso, there are certain techs, by researching them, you research other techs faster. I think if you research like advanced computing, then a few of the minature techs, and then planetary invasions, other things should go faster. Just try and fiddle around with which techs would help you improve research rates.

If there are wars, you just buy your military ships. It would be cheaper and faster. The best thing is to get all the minature techs as fast as possible. this way, you can put more stuff in ships which would compensate for having low level fire power techs.

Specialization is more effective but also requires more player effort and management. I tend to specialize but lately I've been putting 1 farm and 1 stock market on anything PQ7 or better even if that planet is going to be a monster research or manufacturing planet (and yeah sometimes depending on the victory I'm going for I've turned PQ15+ planets into research monsters). Part of the reason for the farm is that since I tend to grab econ and morale racials keeping 11 - 16 billion people happy doesn't take any moral boosters and it generates enough money even with just 1 stock market to support several factories/labs so the planet isn't drawing the treasury down and sometimes 1 or 2 more factories won't actually speed the production of ships anyway.

The farm everywhere giving the stronger pop base makes everything harder to invade as well and allows more transports to be built/bought without much worry. A PQ10 with initial colony, starport, farm, stock market, 4xfactory, and 1xpower plant is actually self sustaining until industrial sectors I believe (if the pop is maxed) and can still crank out medium and large hulls in reasonable time. Killing the farm and the stock market for 2 more factories will cut build times only 3-4 weeks maybe on those ships, though the better the factory tech the more impact those 2 tiles have, if I'm sticking with older factory tech it doesn't help as much.

I've tended to put at least a basic factory or 2 on my econ planets so that auto-upgrades of the econ buildings happen faster, but those factories tend to get upgraded to morale structures later on or if morale is good more stock markets.

But I'll end up with about an 80/20 mix of specialized and generalized planets. The more generalized planets are generally because of tile bonuses as I generally can't get myself to not use the bonus even when I know I'd be better off ignoring it.

I've not been successful with all factories or all labs yet but I'm also generally only about 25% win rate on crippling right now as well so I'm still toying with everything.

That's almost the same as telling someone who is losing a military battle to "just build massive hulled ships with black hole guns and zero point armor"...

You could try the All Factories approach. Of course its a tough start, but once you get going nothing can really touch you on Research or money.

When you start playing Twilight if your not already, if you thought the money problems are bad in DA. DA is a cake walk compared to TA Economy.

Look around for it in the forums. Few Threads that are devoted to A Factories laying around somewhere.

If you focus your factory output to research, 25% is converted.
It's part of the "all factory" strategy, you build only factories, and put your research slider down to 0%, then you focus all planets on research. That way, you only have to build factories and don't waste any of their "potential" production. (A quirk in the way the sliders are configured means that if you put research at say 33%, that means your factories are only poducing 67% of their max output and your labs only 33%. As most buildings also have maintenance costs, this is wasted production per tile/maintenance.)
However, this strategy is a downright pain in the bum as far as I'm concerned, never seem to be able to get the promised benefit over my "normal" management. It's perfectly possible to play up to (at least Obscene) without using an "all X" strategy. I'd recommend not using it until you understand the processes behind the game economics through and through.